When trying to finalize a genome to completion it can be necessary to resequence areas and generate supplementary sequences to close the gaps. After the initial de novo assembly, the result may be up to thousands of contigs, depending on the quality of the reads and the size of the genome. In cases with a reference sequence being available, it may be necessary to sort out potential differences between the reference and sequenced genome or to fill out regions with missing data. In addition, in cases with or without a reference genome being available for alignment of the contigs, it may be necessary to extend the assembled reads. For these purposes the Create Amplicons
tool and Create Primers
tools can be useful.
Create Amplicons is a tool that allows the addition of amplicon annotations to a sequence of interest. These annotations can subsequently be used as target for the Create Primers tool. The advantage of using the Create Amplicons tool prior to primer design is that the Create Amplicons tool can subdivide regions of interest into fragments of suitable sizes.